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Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules onto the surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of 82° on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ((OH)2-SAM). This hydrophobicity, verified by a water slip phenomenon characterizing the friction on the (OH)2-SAM surface, is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of (OH)2-SAM, which sharply reduces the hydrogen bonds between the surface and the water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecule binding to cell adhesion.

Using molecular dynamics simulations, we have studied the effects of salt on the association behavior of solute molecules in nanoconfined aqueous solutions. Three types of solute association states – dispersion, reversible and aggregation states – are still observed in nanoconfined aqueous solutions in the presence of salt. With the increase of ion concentration, the tendency toward the formation of larger clusters is enhanced and the solute critical aggregation number decreases. We even found the transformation of solute association state from the dispersion to the reversible state or from the reversible to the aggregation state within an intermediate range of solute number. This phenomenon is similar to the salting out process and is attributed to the decrease of free water molecules induced by the ion polarization.

Previous work showed that solid polar surfaces with a very small dipole length still might be quite hydrophobic even with large values of charge. Using molecular dynamics simulations, we have found that the presence of the point defects on a solid polar surface greatly influences the wetting behavior of water, even at a very low defect ratio of 1%. As the defect ratio increases, the coverage of the water layer over the solid surface also increases. Because of the breakdown of steric exclusion, the water molecules strongly bind to the solid surface mainly through electrostatic interactions between their hydrogen atoms and the negative charges near the positive-vacancy defects on the surface, or between their oxygen atoms and the positive charges near the negative-vacancy defects.

Phase transitions of water molecules are commonly expected to occur only under extreme conditions, such as nanoconfinement, high pressure, or low temperature. We herein report the disordered-ordered phase transition of two-dimensional interfacial water molecules under ambient conditions using molecular-dynamics simulations. This phase transition is greatly dependent on the charge dipole moment, production of both charge values, and the dipole length of the solid surface. The phase transition can be identified by a sharp change in water-water interaction energies and the order parameters of the two-dimensional interfacial water monolayer, under a tiny dipole moment change near the critical dipole moment. The critical dipole moment of the solid material surface can classify a series of materials that can induce distinct ordered phases of surface water, which may also result in surface wetting, friction, and other properties.

We present atomistic molecular dynamics simulation study of the self-assembly behavior of toll-like agonist lipopeptides (Pam nCSK4) in aqueous solutions. The variable number of hexadecyl lipid chains ( n = 1, 2, 3) per molecule has been experimentally suggested to have remarkable influence on their self-assembled nanostructures. Starting from preassembled spherical or bilayer configurations, the aggregates of lipopeptides, PamCSK4 and Pam2CSK4, which contain peptide sequences CSK4 linked to either mono- or dilipid chains (Pam), evolve into spherical-like micelles within 30 ns, whereas the self-assembled structure of trilipidated lipopeptides, Pam3CSK4, relaxes much slower and reaches an equilibrium state of flattened wormlike micelle with a bilayer packing structure. The geometric shapes and sizes, namely the gyration radii of spherical micelles and thickness of the flattened wormlike micelle, are found to be in good agreement with experimental measurements, which effectively validates the simulation models and employed force fields. Detailed analyses of molecular packing reveal that these self-assembled nanostructures all consist of a hydrophobic core constructed of lipid chains, a transitional layer, and a hydrophilic interfacial layer composed of peptide sequences. The average area per peptide head at the interfaces is found to be nearly constant for all micellar structures studied. The packing parameter of the lipopeptide molecules thus increases with the increase of the number of linked lipid chains, giving rise to the distinct micellar shape transition from spherical-like to flattened wormlike geometry with bilayer stacking, which is qualitatively different from the shape transitions of surfactant micelles induced by variation of concentration or salt type. To facilitate the close-packing of the lipid chains in the hydrophobic core, the lipopeptide molecules typically take the bent conformation with average tilt angles between the peptide sequences and the lipid chains ranging from 110° to 140°. This consequently affects the orientation angles of the lipid chains with respect to the radial or normal direction of the spherical-like or flattened wormlike micelles. In addition, the secondary structures of the peptides may also be altered by the number of lipid chains to which they are linked and the resultant micellar structures. Our simulation results on the microscopic structural features of the lipopeptide nanostructures may provide potential insights into their bioactivities and contribute to the design of bioactive medicines or drug carriers. The force fields built for these lipopeptides and the geometric packing discussions could also be adopted for simulating and understanding the self-assembly behavior of other bioactive amiphiphiles with similar chemical compositions.

Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on GO surfaces. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and π-π stacking interactions, with preferential binding to the oxidized rather than to the unoxidized region of the GO surface. The adsorption process shows a dynamic cooperation adsorption behavior; the ssDNA segment first captures the oxidized groups of the GO surface by hydrogen bonding interaction, and then the configuration relaxes to maximize the π-π stacking interactions between the aromatic rings of the nucleobases and those of the GO surface. We attributed this behavior to the faster forming hydrogen bonding interaction compared to π-π stacking; the π-π stacking interaction needs more relaxation time to regulate the configuration of the ssDNA segment to fit the aromatic rings on the GO surface.

The evaporation of a tiny amount of water on the solid surface with different wettabilities has been studied by molecular dynamics simulations. From nonequilibrium MD simulations, we found that, as the surface changed from hydrophobic to hydrophilic, the evaporation speed did not show a monotonic decrease as intuitively expected, but increased first, and then decreased after it reached a maximum value. The analysis of the simulation trajectory and calculation of the surface water interaction illustrate that the competition between the number of water molecules on the water-gas surface from where the water molecules can evaporate and the potential barrier to prevent those water molecules from evaporating results in the unexpected behavior of the evaporation. This finding is helpful in understanding the evaporation on biological surfaces, designing artificial surfaces of ultrafast water evaporating, or preserving water in soil.

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.

Molecular dynamic simulations of the chiral transition of a difluorobenzo[c]phenanthrene molecule (C(18)H(12)F(2), D molecule) in single-walled boron-nitride nanotubes (SWBNNTs) revealed remarkable effects of the nanoscale confinement. The critical temperature, above which the chiral transition occurs, increases considerably with the nanotube diameter, and the chiral transition frequency decreases almost exponentially with respect to the reciprocal of temperature. The chiral transitions correlate closely with the orientational transformations of the D molecule. Furthermore, the interaction energy barriers between the D molecule and the nanotube for different orientational states can characterize the chiral transition. This implies that the temperature threshold of a chiral transition can be controlled by a suitable nanotube. These findings provide new insights to the effect of nanoscale confinement on molecular chirality.

Confinement of molecules inside nanoscale pores has become an important method for exploiting new dynamics not happening in bulk systems and for fabricating novel structures. Molecules that are encapsulated in nanopores are difficult to control with respect to their position and activity. On the basis of molecular dynamics simulations, we have achieved controllable manipulation, both in space and time, of biomolecules with aqueous liquids inside a single-walled nanotube by using an external charge or a group of external charges. The remarkable manipulation abilities are attributed to the single-walled structure of the nanotube that the electrostatic interactions of charges inside and outside the single-walled nanotube are strong enough, and the charge-induced dipole-orientation ordering of water confined in the nanochannel so that water has a strong interaction with the external charge. These designs are expected to serve as lab-in-nanotube for the interactions and chemical reactions of molecules especially biomolecules, and have wide applications in nanotechnology and biotechnology.

Using molecular dynamics simulations, we show that an asymmetrically shaped nanoparticle in dilute solution possesses a spontaneously curved trajectory within finite time interval, instead of the generally expected random walk. This unexpected dynamic behavior has a similarity to that of active matters, such as swimming bacteria, cells or even fishes, but is of a different physical origin. The key to the curved trajectory lies in the non-zero resultant force originated from the imbalance of the collision forces acted by surrounding solvent molecules on the shaped nanoparticle during its orientation regulation. Theoretical formulae based on the microscopic observation have been derived to describe this non-zero force and the resulted motion of the nanoparticle., Comment: 7 pages, 2 figures

Using molecular dynamics simulations, we find a reversible transition between the dispersion and aggregation states of solute molecules in aqueous solutions confined in nanoscale geometry, which is not observed in macroscopic systems. The nanoscale confinement also leads to a significant increase of the critical aggregation concentration (CAC). A theoretical model based on Gibbs free energy calculation is developed to describe the simulation results. It indicates that the reversible state transition is attributed to the low free energy barrier (of order k(B)T) in between two energy minima corresponding to the dispersion and aggregation states, and the enhancement of the CAC results from the fact that at lower concentrations the number of solute molecules is not large enough to allow the formation of a stable cluster in the confined systems.

The wetting behavior of water on the solid surfaces is fundamental to various physical, chemical and biological processes. Conventionally, the surface with charges or charge dipoles is hydrophilic, whereas the non-polar surface is hydrophobic though some exceptions were recently reported. Using molecular dynamics simulations, we show that there is a critical length of the charge dipoles on the solid surface. The solid surface still exhibited hydrophobic behavior when the dipole length was less than the critical value, indicating that the water molecules on the solid surface seemed not “feel” attractive interactions from the charge dipoles on the solid surface. Those unexpected observations result from the collective interactions between the water molecules and charge dipoles on the solid surface, where the steric exclusion effect between water molecules greatly reduces the water-dipole interactions. Remarkably, the steric exclusion effect is also important for surfaces with charge dipole lengths greater than this critical length.

The dynamics of water molecules confined in nanochannels is of great importance for designing novel molecular devices/machines/sensors, which have wide applications in nanotechnology, such as water desalination, chemical separation, sensing. In this chapter, inspired by the aquaporins, which are proteins embedded in the cell membrane that regulate the flow of water but stop the protons, we will discuss the mechanism of water channel gating and water channel pumping, where water molecules form single-filed structure. The single-filed water molecules can also serve as molecular devices for signal transmission, conversion, and multiplication. Moreover, the water in the channel may have great potential applications in designing the lab-in-tube to controllable manipulation of biomolecules.

It is believed that water anomalies are related to the hydrogen bonds between water molecules, but the relationship still remains a challenge. Here, by introducing two types of hydrogen bond--strong and weak, we successfully reproduce many liquid water anomalies, particularly the thermodynamic anomalies at supercooled temperature. We find that the exchange of strong and weak H bonds, which enhance the competition between the open and collapsed structures of liquid water, might be the key to those anomalies of supercooled liquid water. Our study is helpful in understanding the hydrogen bond structure in liquid water.

The diffusion of an ammonia molecule (NH3) in water was investigated by molecular dynamic simulations. It is found that the diffusion shows negative correlation with its dipole orientation.